Merge branch 'master' into jp-3005-pixel-replacement

hbushouse · web-flow · commit ff1185d48e42 · 2023-04-13T13:57:06.000-04:00
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,4 +1,4 @@
-1.10.1 (unreleased)
+1.10.1 (2023-04-13)
 ===================
 
 documentation
@@ -18,6 +18,13 @@ flat_field
 
 - Updated to allow processing of NIRSpec fixed-slit 3D (rateints) files. [#7516]
 
+jump
+----------
+- Added a new parameter that limits maximum size of extension of jump. It exists
+  in the STCAL jump code but not in JWST. This allows the parameter to be changed.
+  Also, scaled two input parameters that are listed as radius to be a factor of two
+  higher to match the opencv code that uses diameter. [#7545]
+  
 other
 -----
 
diff --git a/CITATION.cff b/CITATION.cff
@@ -72,7 +72,7 @@ authors:
   given-names: "Thomas"
   orcid: "https://orcid.org/0000-0002-0012-2142"
 title: "JWST Calibration Pipeline"
-version: 1.10.0
+version: 1.10.1
 doi: 10.5281/zenodo.7038885
-date-released: 2023-04-03
+date-released: 2023-04-13
 url: "https://github.com/spacetelescope/jwst"
diff --git a/README.md b/README.md
@@ -215,6 +215,7 @@ the specified context and less than the context for the next release.
 
 | jwst tag            | DMS build | SDP_VER  | CRDS_CONTEXT | Released   | Ops Install | Notes                                         |
 |---------------------|-----------|----------|--------------|------------|-------------|-----------------------------------------------|
+| 1.10.1              | B9.2rc2   | TBD      | 1077         | 2023-04-13 | TBD         | Second release candidate for B9.2             |
 | 1.10.0              | B9.2rc1   | TBD      | 1075         | 2023-03-31 | TBD         | First release candidate for B9.2              |
 | 1.9.6               | B9.1.2    | 2022.5.2 | 1068         | 2023-03-09 | 2023-03-15  | Final release candidate for B9.1.2            |
 | 1.9.5               |           |          | 1061         | 2023-03-02 |             | First release candidate for B9.1.2            |
diff --git a/docs/jwst/jump/arguments.rst b/docs/jwst/jump/arguments.rst
@@ -80,3 +80,5 @@ The ``jump`` step has five optional arguments that can be set by the user:
 * ``--extend_ellipse_expand_ratio``: Multiplicative factor to expand the radius of the ellipse fit to the detected extended emission in MIRI showers
 
 * ``--time_masked_after_showers``: Number of seconds to flag groups as jump after a detected extended emission in MIRI showers
+
+* ``--max_extended_radius``: The maxiumum extension of the jump and saturation that will be flagged for showers or snowballs
diff --git a/jwst/jump/jump.py b/jwst/jump/jump.py
@@ -23,7 +23,8 @@ def run_detect_jumps(input_model, gain_model, readnoise_model,
                      sat_required_snowball=True, sat_expand=2,
                      expand_large_events=False, find_showers=False, edge_size=25, extend_snr_threshold=1.1,
                      extend_min_area=90, extend_inner_radius=1, extend_outer_radius=2.6, extend_ellipse_expand_ratio=1.1,
-                     time_masked_after_shower=30
+                     time_masked_after_shower=30,
+                     max_extended_radius=200,
                      ):
 
     # Runs `detect_jumps` in stcal
@@ -77,7 +78,9 @@ def run_detect_jumps(input_model, gain_model, readnoise_model,
                                     extend_min_area=extend_min_area, extend_inner_radius=extend_inner_radius,
                                     extend_outer_radius=extend_outer_radius,
                                     extend_ellipse_expand_ratio=extend_ellipse_expand_ratio,
-                                    grps_masked_after_shower=grps_masked_after_shower)
+                                    grps_masked_after_shower=grps_masked_after_shower,
+                                    max_extended_radius=max_extended_radius)
+
 
     # Update the DQ arrays of the output model with the jump detection results
     output_model.groupdq = new_gdq
diff --git a/jwst/jump/jump_step.py b/jwst/jump/jump_step.py
@@ -42,6 +42,7 @@ class JumpStep(Step):
         extend_outer_radius = float(default=2.6) Outer radius of the ring_2D_Kernel used for convolution
         extend_ellipse_expand_ratio = float(default=1.1) Expand the radius of the ellipse fit to the extended emission
         time_masked_after_shower = float(default=15) Seconds to flag as jump after a detected extended emission
+        max_extended_radius = integer(default=200) The maximum radius of an extended snowball or shower
     """
 
     reference_file_types = ['gain', 'readnoise']
@@ -107,14 +108,16 @@ def process(self, input):
                                       min_sat_area=min_sat_area, min_jump_area=min_jump_area,
                                       expand_factor=expand_factor, use_ellipses=use_ellipses,
                                       min_sat_radius_extend=self.min_sat_radius_extend,
-                                      sat_required_snowball=sat_required_snowball, sat_expand=self.sat_expand,
+                                      sat_required_snowball=sat_required_snowball, sat_expand=self.sat_expand * 2,
                                       expand_large_events=expand_large_events, find_showers=self.find_showers,
                                       edge_size=self.edge_size, extend_snr_threshold=self.extend_snr_threshold,
                                       extend_min_area=self.extend_min_area,
                                       extend_inner_radius=self.extend_inner_radius,
                                       extend_outer_radius=self.extend_outer_radius,
                                       extend_ellipse_expand_ratio=self.extend_ellipse_expand_ratio,
-                                      time_masked_after_shower=self.time_masked_after_shower)
+                                      time_masked_after_shower=self.time_masked_after_shower,
+                                      max_extended_radius=self.max_extended_radius * 2)
+
 
             gain_model.close()
             readnoise_model.close()
diff --git a/requirements-sdp.txt b/requirements-sdp.txt
@@ -14,3 +14,99 @@
 #     conda activate sdp
 #     pip install -e .[test,sdp]
 #     pip freeze | grep -v jwst >> requirements-sdp.txt
+alabaster==0.7.13
+asdf==2.15.0
+asdf-astropy==0.4.0
+asdf-coordinates-schemas==0.2.0
+asdf-standard==1.0.3
+asdf-transform-schemas==0.3.0
+asdf-unit-schemas==0.1.0
+asdf-wcs-schemas==0.1.1
+astropy==5.2.2
+attrs==22.2.0
+Babel==2.12.1
+BayesicFitting==3.1.1
+certifi==2022.12.7
+charset-normalizer==3.1.0
+ci-watson==0.6.1
+colorama==0.4.6
+contourpy==1.0.7
+coverage==7.2.3
+crds==11.16.22
+cycler==0.11.0
+docutils==0.19
+drizzle==1.13.7
+et-xmlfile==1.1.0
+exceptiongroup==1.1.1
+filelock==3.11.0
+fonttools==4.39.3
+future==0.18.3
+gwcs==0.18.3
+idna==3.4
+imageio==2.27.0
+imagesize==1.4.1
+importlib-metadata==6.3.0
+importlib-resources==5.12.0
+iniconfig==2.0.0
+Jinja2==3.1.2
+jmespath==1.0.1
+jplephem==2.18
+jsonschema==4.17.3
+kiwisolver==1.4.4
+lazy_loader==0.2
+lxml==4.9.2
+MarkupSafe==2.1.2
+matplotlib==3.7.1
+networkx==3.1
+numpy==1.24.2
+numpydoc==1.5.0
+opencv-python==4.7.0.72
+openpyxl==3.1.2
+packaging==23.1
+Parsley==1.3
+photutils==1.7.0
+Pillow==9.5.0
+pluggy==1.0.0
+poppy==1.0.3
+psutil==5.9.4
+pyerfa==2.0.0.3
+Pygments==2.15.0
+pymssql==2.2.7
+pyparsing==3.0.9
+pyrsistent==0.19.3
+pysiaf==0.19.1
+pytest==7.3.0
+pytest-cov==4.0.0
+pytest-doctestplus==0.12.1
+python-dateutil==2.8.2
+PyWavelets==1.4.1
+PyYAML==6.0
+readchar==4.0.5
+requests==2.28.2
+requests-mock==1.10.0
+ruff==0.0.261
+scikit-image==0.20.0
+scipy==1.9.1
+semantic-version==2.10.0
+six==1.16.0
+snowballstemmer==2.2.0
+spherical-geometry==1.2.23
+Sphinx==6.1.3
+sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+stcal==1.3.5
+stdatamodels==1.3.1
+stpipe==0.4.6
+stsci.image==2.3.5
+stsci.imagestats==1.6.3
+stsci.stimage==0.2.6
+tifffile==2023.4.12
+tomli==2.0.1
+tweakwcs==0.8.1
+urllib3==1.26.15
+wiimatch==0.3.1
+zipp==3.15.0
